Commit 19cac6d0 authored by Mohamed, Fawzi Roberto (fawzi)'s avatar Mohamed, Fawzi Roberto (fawzi)
Browse files

fixing tests

parent 12a0fc4f
...@@ -211,7 +211,7 @@ class Section(object): ...@@ -211,7 +211,7 @@ class Section(object):
else: else:
logger.error("The subsection '{}' in '{}' has too many entries.".format(name, self.name)) logger.error("The subsection '{}' in '{}' has too many entries.".format(name, self.name))
else: else:
logger.error("The subsection '{}' in '{}' does not exist.".format(name, self.name)) logger.error("The subsection '{}' in '{}' does not exist, knowing sections {} and keywords {} .".format(name, self.name, self.sections.keys(), self.keywords.keys()))
def get_subsection_list(self, name): def get_subsection_list(self, name):
subsection = self.sections.get(name) subsection = self.sections.get(name)
......
...@@ -41,6 +41,7 @@ class CP2KGeoOptParser(MainHierarchicalParser): ...@@ -41,6 +41,7 @@ class CP2KGeoOptParser(MainHierarchicalParser):
#======================================================================= #=======================================================================
# Globally cached values # Globally cached values
self.cache_service.add("number_of_frames_in_sequence", 0) self.cache_service.add("number_of_frames_in_sequence", 0)
self.cache_service.add("frame_sequence_potential_energy", [])
self.cache_service.add("frame_sequence_to_frames_ref", []) self.cache_service.add("frame_sequence_to_frames_ref", [])
self.cache_service.add("geometry_optimization_method") self.cache_service.add("geometry_optimization_method")
self.cache_service.add("geometry_optimization_converged") self.cache_service.add("geometry_optimization_converged")
...@@ -195,7 +196,7 @@ class CP2KGeoOptParser(MainHierarchicalParser): ...@@ -195,7 +196,7 @@ class CP2KGeoOptParser(MainHierarchicalParser):
if reeval_quickstep is not None: if reeval_quickstep is not None:
energy = reeval_quickstep.get_latest_value("x_cp2k_energy_total") energy = reeval_quickstep.get_latest_value("x_cp2k_energy_total")
if energy is not None: if energy is not None:
self.backend.addValue("potential_energy", energy) self.cache_service["frame_sequence_potential_energy"].append(energy)
# Push values from cache # Push values from cache
self.cache_service.addValue("geometry_optimization_method") self.cache_service.addValue("geometry_optimization_method")
...@@ -231,6 +232,7 @@ class CP2KGeoOptParser(MainHierarchicalParser): ...@@ -231,6 +232,7 @@ class CP2KGeoOptParser(MainHierarchicalParser):
n_steps -= 1 n_steps -= 1
last_step = n_steps - 1 last_step = n_steps - 1
ePot = self.cache_service['frame_sequence_potential_energy']
# First push the original system geometry # First push the original system geometry
# print(self.cache_service["atom_positions"]) # print(self.cache_service["atom_positions"])
for i_step in range(n_steps): for i_step in range(n_steps):
...@@ -252,6 +254,7 @@ class CP2KGeoOptParser(MainHierarchicalParser): ...@@ -252,6 +254,7 @@ class CP2KGeoOptParser(MainHierarchicalParser):
else: else:
backend.addArrayValues("atom_positions", pos, unit="angstrom") backend.addArrayValues("atom_positions", pos, unit="angstrom")
backend.closeSection("section_system", systemId) backend.closeSection("section_system", systemId)
backend.addValue("potential_energy", ePot[i_step])
backend.closeSection("section_single_configuration_calculation", singleId) backend.closeSection("section_single_configuration_calculation", singleId)
self.cache_service.addArrayValues("frame_sequence_to_frames_ref") self.cache_service.addArrayValues("frame_sequence_to_frames_ref")
...@@ -269,7 +272,7 @@ class CP2KGeoOptParser(MainHierarchicalParser): ...@@ -269,7 +272,7 @@ class CP2KGeoOptParser(MainHierarchicalParser):
def onClose_x_cp2k_section_geometry_optimization_step(self, backend, gIndex, section): def onClose_x_cp2k_section_geometry_optimization_step(self, backend, gIndex, section):
energy = section["x_cp2k_optimization_energy"] energy = section["x_cp2k_optimization_energy"]
if energy is not None: if energy is not None:
self.backend.addValue("potential_energy",energy[0]) self.cache_service["frame_sequence_potential_energy"].append(energy[0])
def onClose_section_system(self, backend, gIndex, section): def onClose_section_system(self, backend, gIndex, section):
self.cache_service.addArrayValues("simulation_cell", unit="angstrom") self.cache_service.addArrayValues("simulation_cell", unit="angstrom")
......
...@@ -361,14 +361,14 @@ class CP2KMDParser(MainHierarchicalParser): ...@@ -361,14 +361,14 @@ class CP2KMDParser(MainHierarchicalParser):
wall_time = line[6] wall_time = line[6]
frame_sequence_time.append(time) frame_sequence_time.append(time)
backend.addValue('kinetic_energy', kinetic_energy, unit="hartree") backend.addRealValue('kinetic_energy', kinetic_energy, unit="hartree")
backend.addValue('instant_temperature', temperature, unit="K") backend.addRealValue('instant_temperature', temperature, unit="K")
backend.addValue('potential_energy', potential_energy, unit="hartree") backend.addRealValue('potential_energy', potential_energy, unit="hartree")
backend.addValue('conserved_quantity', conserved_quantity, unit="hartree") backend.addRealValue('conserved_quantity', conserved_quantity, unit="hartree")
ener_frames.append(i_step) ener_frames.append(i_step)
backend.addValue("energy_total", conserved_quantity, unit="hartree") backend.addRealValue("energy_total", conserved_quantity, unit="hartree")
backend.addValue("time_calculation", wall_time) backend.addValue("time_calculation", wall_time)
# Cell file # Cell file
......
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